DEPRECATED: Visit FOSS-2020 for current pages

CyVerse Learning Institute - Foundational Open Science Skills (FOSS) 2019

Foundational Open Science Skills (FOSS) is a novel, camp-style training designed to prepare principal investigators and their lab teams, both new and established, to meet the growing expectations of funding agencies, publishers, and research institutions for scientific reproducibility and data accessibility.

Prior to the workshop, please visit the Before you arrive page.

Workshop Level

There are no pre-requisites for FOSS, but the course will cover a lot of material in a short time. Participants who have limited computational experience should try to view the Software Carpentry Core Lessons before attending.

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Expected outcomes:

• Familiarity with productivity software for organizing your lab group, communications, and research
• How to scale out your computation from laptop to cloud and high performance computing (HPC) systems
• How to manage data for open science and reproducibility

• FOSS 2019 Home

Before you Arrive

• Before you arrive
• Pre-Workshop Setup
• About CyVerse

Getting Started

• FOSS 2019 Introduction
• Code of Conduct
• Agenda
• Open Science Lab
• Glossary & Acronyms

Software Essentials

• Basics of Linux
• Version Control
• Lab Group Communication
• Websites & Documentation
• Command Line and the Unix Shell
• Introduction to R & RStudio
• RStudio with Version Control
• Continuous Integration

CyVerse

• Introduction to CyVerse
• Discovery Environment
• CyVerse Data Store
• VICE
• Atmosphere
• Tool Integration into the DE

Data Management

• Data Management Overview
• FAIR Data
• Data Management Plans (DMP)

Moving On

• Research Cyberinfrastructure associated with CyVerse
• Other Cyberinfrastructure Projects

Containers

• Launching a Docker app on Atmosphere
• Introduction to BioContainers
• Introduction to Docker
• Advanced Docker

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Course Instructors

• Amanda Cooksey
• Tina Lee
• Tyson Swetnam
• Ramona Walls

Guest instructors:

• Fernando Rios (UA Libraries)
• Michael Mandel (UA Eller College of Management)

About CyVerse

CyVerse Vision: Transforming science through data-driven discovery.

CyVerse Mission: Design, deploy, and expand a national cyberinfrastructure for life sciences research and train scientists in its use.

CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Our powerful extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, APIs, and more.

While originally created with the name iPlant Collaborative to serve U.S. plant science communities, CyVerse cyberinfrastructure is germane to all life sciences disciplines and works equally well on data from plants, animals, or microbes. By democratizing access to supercomputing capabilities, we provide a crucial resource to enable scientists to find solutions for the future.

CyVerse Homepage: http://www.cyverse.org

Funding and Citations

CyVerse is funded by the National Science Foundation under Award Numbers DBI-0735191, DBI-1265383, and DBI-1743442.

Please cite CyVerse appropriately when you make use of our resources, CyVerse citation policy

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Fix or improve this documentation

• Search for an answer: CyVerse Learning Center
• Ask us for help: click on the lower right-hand side of the page
• Report an issue or submit a change: |Github Repo Link|
• Send feedback: Tutorials@CyVerse.org

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